Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: bioinfblog@gmail.com and get the word out!

Thursday, January 05, 2006

PSB 2006
Michael Ashburner, "Ontologies for biologists - A community model for the annotation of genomic data"
One of the originators of the GO ontology, Dr. Ashburner talked about the intial planning and development of the GO ontology and how it (and everything in bioinformatics) should follow the "Manifesto of liberation of bioinformatics":
-Be open source.
-Use open standards.
-Make data and code available without constraint.
-Involve your community.

He also noted that in the near future there will be links between the three main categories in the GO ontology (geneontology.org) meaning there will be interrelationships between molecular functions, biological processes, and locations. For me, this means more headache for developing methods that must utilize the now more complex (interrelated) heirarchy of the ontology. It seems from this talk that the future is more and more ontologies that are all linked together somehow. He mentions that there are many specialized ontologies that are popping up that augment GO. Think things like neuro ontology and ligand ontology (author's ideas not Dr. Ashburner's); moreover these ontologies are linked and launched through efforts like the national center for biomedical ontology.

Perhaps the most successful type of new ontology (well I'll assume it's the most successful because it's the only other one he got into) is Sequence Ontology or (SO). Here sequences are annotated with different features for different locations on the sequence with a defined ontological heirarchy. He mentions attributes encompassing sequence attributes, mutational consequences, and chromosomal variation.
All in all it was an interesting talk about the future of biological ontologies, which, in my view, is a pretty much thankless job but very important to the field. Think over 1000 citations on Scholar.

23 Comments:

Blogger Francis Crick said...

Hmm interesting. I hope they are satisfied with maximum accuracy/completeness of the existing data and connections in GO before making more networks beyond the current ones. But I think this is a common critique of systems bio in general...

12:17 PM  
Blogger The Bioinformatics Blog said...

Ya he mentioned that one approach is community annotation, which for the most part he forwned upon. He talked about Gene ontology developers (GODs!) as the main people annotating. This is kind of akin to wikipedia where there are a few people who do most of the annotating.

4:55 PM  
Anonymous Anonymous said...

[url=http://www.kfarbair.com][img]http://www.kfarbair.com/_images/logo.png[/img][/url]

בית מלון [url=http://www.kfarbair.com]כפר בעיר[/url] - שירות חדרים אנו מספקים שירותי אירוח מגוונים גם ישנו במקום שירות חדרים המכיל [url=http://www.kfarbair.com/eng/index.html]אחרוחות רומנטיות[/url] במחירים מיוחדים אשר יוגשו ישירות לחדרכם...

לפרטים נוספים אנא לפנות לעמוד המלון - [url=http://kfarbair.com]כפר בעיר[/url] [url=http://www.kfarbair.com/contact.html][img]http://www.kfarbair.com/_images/apixel.gif[/img][/url]

4:05 PM  
Anonymous Anonymous said...

Greetings www.blogger.com people.

Are you looking to get your Site [b]Listed on top of MSN[/b] search engine? Maybe you are looking to get more traffic? We have the perfect deal for you! We offer you an exclusive chance to experiance the knowledge of our [b][url=http://xrumer-blast.com/marketplace/xrumer-products/]Xrumer Services[/url][/b]. [url=http://www.xrumer-blast.com][img]http://xrumer-blast.com/wp-includes/images/smilies/icon_smile.gif[/img][/url]

This is NOT trash! This is a human created post created specifically to demonstrate the power of our automated software and its potential of getting to wide variety of audience in an effective and time saving manner.

We are a group of veteran [b][url=http://xrumer-blast.com/about-xrumer-blast-com/]Internet Marketers[/url][/b] and [b]SEO Experts[/b] that provide [b]Affordable, High Quality, [url=http://xrumer-blast.com/marketplace/seo-products/]SEO Service[/url][/b]. Post your message on thousands of forums, message boards, blogs and journals and gain organic traffic in a matter of days! With the help of our [b][url=http://xrumerblast.livejournal.com/]Search Engine Optimization Experts[/url][/b] your [b]Store URL[/b] can appear on [b]4236[/b] message boards and journals. Receive almost instant growth of your search engine position, Get thousands of quality backlinks directly to your Site without lifting a finger!

Our goal is simple; we want to make you and your website on the top of every search engine so you and your family can enjoy the comfort of steady, automatic income without leaving your home. Trough our [b][url=http://xrumer-blast.com/contact-xrumer-blast-com/]SEO Experts Advice[/url][/b] you will get one of the best support seen in the industry. As part of our [b]Search Engine Optimization Services[/b], we take care of everything for you, from Optimizing your Website for search engines all through ranking your Site on the first page of your MSN.

For more information regarding [b]Search Engine Optimiztion[/b] and [b]Xrumer Blast Services[/b] check out [b][url=http://xrumerservice2010.wordpress.com/]Xrumer Blast[/url][/b]. Our site includes everything you need to order your first [b]Xrumer Blast[/b], you can create the most appropriate message (Project) to suit your Website, send us the information and after the payment clearance we will start working immediatly!

[url=http://xrumer-blast.com/marketplace/][img]http://xrumer-blast.com/wp-content/uploads/Xrumer-Blast-Logo.png[/img][/url]

4:29 PM  
Anonymous Anonymous said...

I have not checked in here for some time as I thought it was getting boring,
but the last several posts are great quality so I guess I
will add you back to my everyday bloglist. You deserve it my
friend :)

Here is my website - how to breed in dragonvale

9:02 PM  
Anonymous Anonymous said...

Amazing! Its genuinely awesome piece of writing, I have got much clear idea regarding from this post.


Here is my webpage ... linkbucks bot

10:48 PM  
Anonymous Anonymous said...

Wow, wonderful weblog format! How lengthy have you
ever been running a blog for? you made blogging look easy.
The full look of your web site is fantastic, let
alone the content material!

My site ... twitter account

7:48 AM  
Anonymous Anonymous said...

I got what you mean , appreciate it for putting up.
Woh I am happy to find this website through google. "Wisdom doesn't necessarily come with age. Sometimes age just shows up by itself." by Woodrow Wilson.


Also visit my homepage; aimbot download

1:19 AM  
Anonymous Anonymous said...

Hello, I would like to subscribe for this web site to take most
up-to-date updates, thus where can i do it please assist.


Feel free to visit my blog ... password cracker

7:54 AM  
Anonymous Anonymous said...

Touche. Sound arguments. Keep up the good spirit.

My web page Recover Twitter Account

9:09 PM  
Anonymous Anonymous said...

This text is invaluable. When can I find out more?


Here is my webpage ... miscrits rare

9:23 AM  
Anonymous Anonymous said...

Link exchange is nothing else however it is just placing the other person's webpage link on your page at proper place and other person will also do similar for you.

Visit my weblog - download sharecash

8:46 PM  
Anonymous Anonymous said...

Hi! I know this is kinda off topic nevertheless
I'd figured I'd ask. Would you be interested in exchanging links or maybe guest writing a blog article or vice-versa?

My website addresses a lot of the same topics as yours and I think we could greatly benefit from each other.
If you're interested feel free to shoot me an email. I look forward to hearing from you! Superb blog by the way!

My web page :: money maker

7:06 AM  
Anonymous Anonymous said...

Hey there! Do you use Twitter? I'd like to follow you if that would be ok. I'm absolutely enjoying your blog and look forward to new posts.


Here is my web page: lost password

8:34 AM  
Anonymous Anonymous said...

Hi there to every , as I am truly eager of reading this website's post to be updated on a regular basis. It contains fastidious information.

Also visit my website ... password hack

11:02 PM  
Anonymous Anonymous said...

I'll immediately seize your rss feed as I can't find your e-mail
subscription hyperlink or e-newsletter service. Do you have any?
Kindly allow me realize in order that I could subscribe. Thanks.



my webpage sharecash auto

12:02 PM  
Anonymous Anonymous said...

What's up, yes this post is genuinely fastidious and I have learned lot of things from it about blogging. thanks.

Feel free to visit my webpage ... adult Games

5:39 AM  
Anonymous Anonymous said...

Fantastic post however I was wanting to
know if you could write a litte more on this subject?

I'd be very grateful if you could elaborate a little bit further. Thank you!

Also visit my web-site :: Online TV Series

1:50 AM  
Anonymous Anonymous said...

Can I simply just say what a comfort to discover a person that truly understands what they are discussing on
the net. You actually realize how to bring a problem to light and make it important.
More and more people ought to check this out and understand this side
of your story. I can't believe you are not more popular since you certainly have the gift.

Have a look at my webpage - hack de castleville

9:51 AM  
Anonymous Anonymous said...

Great post.

Feel free to visit my web page :: forgot twitter password

10:41 AM  
Anonymous Anonymous said...

I don't even know how I ended up here, but I thought this post was good. I do not know who you are but certainly you're going to a famous blogger if
you are not already ;) Cheers!

Feel free to surf to my web-site ... best ptc sites

10:34 PM  
Anonymous Anonymous said...

This text is priceless. How can I find out more?

Here is my webpage - Free Minecraft Download

9:59 PM  
Anonymous Anonymous said...

electronic cigarette, e cig forum, electronic cigarette, best e cigarette, smokeless cigarette, ecig forum

9:28 AM  

Post a Comment

<< Home